com.mysql.jdbc.exceptions.jdbc4.CommunicationsException MySQL + Apache Tomcat 7

Question

My application (Spring 4 MVC / Hibernate 4 / MySQL / Maven) integrates Spring with Hibernate using annotation-based configuration. After a few hours of it not using the database I always see this error:

com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 84,510,841 milliseconds ago.  The last packet sent successfully to the server was 84,510,841 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem.
    sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
    sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    java.lang.reflect.Constructor.newInstance(Constructor.java:526)
    com.mysql.jdbc.Util.handleNewInstance(Util.java:411)
    com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1121)
    com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3938)
    com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2551)
    com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2731)
    com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2809)
    com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:5333)
    sun.reflect.GeneratedMethodAccessor58.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.apache.tomcat.jdbc.pool.ProxyConnection.invoke(ProxyConnection.java:126)
    org.apache.tomcat.jdbc.pool.JdbcInterceptor.invoke(JdbcInterceptor.java:109)
    org.apache.tomcat.jdbc.pool.DisposableConnectionFacade.invoke(DisposableConnectionFacade.java:80)
    com.sun.proxy.$Proxy33.setAutoCommit(Unknown Source)
    org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.begin(AbstractLogicalConnectionImplementor.java:67)
    org.hibernate.resource.jdbc.internal.LogicalConnectionManagedImpl.begin(LogicalConnectionManagedImpl.java:238)
    org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.begin(JdbcResourceLocalTransactionCoordinatorImpl.java:213)
    org.hibernate.engine.transaction.internal.TransactionImpl.begin(TransactionImpl.java:52)
    org.hibernate.internal.SessionImpl.beginTransaction(SessionImpl.java:1512)
    org.hibernate.jpa.internal.TransactionImpl.begin(TransactionImpl.java:45)
    org.springframework.orm.jpa.vendor.HibernateJpaDialect.beginTransaction(HibernateJpaDialect.java:170)
    org.springframework.orm.jpa.JpaTransactionManager.doBegin(JpaTransactionManager.java:380)
    org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:373)
    org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:427)
    org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:276)
    org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96)
    org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
    com.sun.proxy.$Proxy118.findAll(Unknown Source)
    com.ideefe.iot.controller.AppController.listDevices(AppController.java:49)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    java.lang.reflect.Method.invoke(Method.java:606)
    org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:222)
    org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:137)
    org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:110)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:814)
    org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:737)
    org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:85)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:959)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:893)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:970)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:861)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:620)
    org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:846)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:77)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)
    org.springframework.web.multipart.support.MultipartFilter.doFilterInternal(MultipartFilter.java:118)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107)

Here is the MySQL my.cnf file:

devuser@localhost:/etc/apache2$ more /etc/mysql/my.cnf
#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
# 
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port        = 3306
socket      = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket      = /var/run/mysqld/mysqld.sock
nice        = 0

[mysqld]
#
# * Basic Settings
#
user        = mysql
pid-file    = /var/run/mysqld/mysqld.pid
socket      = /var/run/mysqld/mysqld.sock
port        = 3306
basedir     = /usr
datadir     = /var/lib/mysql
tmpdir      = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address        = 127.0.0.1
#
# * Fine Tuning
#
key_buffer      = 32M
max_allowed_packet  = 1M
thread_stack        = 128K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched
myisam-recover         = BACKUP
max_connections        = 75
table_cache            = 32
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit   = 1M
query_cache_size        = 16M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!
#general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#log_slow_queries   = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about
#       other settings you may need to change.
#server-id      = 1
#log_bin            = /var/log/mysql/mysql-bin.log
expire_logs_days    = 10
max_binlog_size         = 100M
#binlog_do_db       = include_database_name
#binlog_ignore_db   = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#
# Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet  = 16M

[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer      = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/

I am using a connection pool defined as follows:

<?xml version="1.0" encoding="UTF-8"?> 
<Context>
    <!-- Especifica un DataSource JDBC. --> 
    <Resource name="jdbc/devicesDS"
              auth="Container"
              type="javax.sql.DataSource"
              maxActive="10"
              maxIdle="4"
              username="root"
              password="SrbBfsatn640^"
              driverClassName="com.mysql.jdbc.Driver"
              url="jdbc:mysql://localhost:3306/devices?autoReconnect=true"
              validationQuery="select 1 from dual" />
</Context>  

Answer 1

Looks like this is the MySQL inactivity timeout - there's quite a few similar StackOverflow questions around it (e.g. here, here and here). Would advise changing your connection pool settings by adding testOnBorrow=true, i.e:

<Resource name="jdbc/devicesDS"
          auth="Container"
          type="javax.sql.DataSource"
          maxActive="10"
          maxIdle="4"
          username="root"
          password="SrbBfsatn640^"
          driverClassName="com.mysql.jdbc.Driver"
          url="jdbc:mysql://localhost:3306/devices?autoReconnect=true"
          validationQuery="select 1 from dual"
          testOnBorrow=true />

I'd personally lean towards testOnBorrow over the alternative of testWhileIdle since the former is completely independent of the wait_timeout value (but not sure how the performance compares). Would also be cautious about using the alternative of autoreconnect=true in the JDBC URL: It isn't recommended by the MySQL Connector/J documentation "because it has side effects related to session state and data consistency when applications don't handle SQLExceptions properly, and is only designed to be used when you are unable to configure your application to handle SQLExceptions resulting from dead and stale connections properly".